I'm familiar with a focal length crop factor of 1.6x for APS-C sensors, but my question is does this affect MFD or maximum magnifcation as well?

I'm specifically curious as i have a non-usm 100mm Macro lens with a 550D but am planning to upgrade to a 5dmk3 and 100L in the near future and am curious how the magnification may change and bokeh.

you are going to notice 2 thing right off the bat

1) it no longer seems to get as close because you lose your 1.6 (note a kenko 1.4 TC will nearly fix this nicely you can also stack it with the extension tubes to get closer still) kenko TC will work with any EF lens unlike the canon ones.2) the Dof will seem unbelievably shallow so you are going to want to stop down anyway therefore adding a TC into the mix wont hurt

I'm familiar with a focal length crop factor of 1.6x for APS-C sensors, but my question is does this affect MFD or maximum magnifcation as well?

Tehcnically, it affects neither - the MFD is a property of the lens, so it will be unchanged. The maximum magnification will remain 1:1.

But, what will change are the field of view and the apparent magnification. A macro lens delivering 1:1 magnification at the MFD is projecting a life-sized image onto the sensor. Because of the smaller sensor, your 550D can capture an opject up to ~22x15mm, whereas the 5DIII will capture a a larger object, up to 36x24mm. But...that's only 4 more MP spread over a larger area, so the pixel density is lower. That means if you shoot the same size object at the same distance (assuming the object is small enough to fit within the APS-C sensor area), when you view both shots at 100% on your monitor, the shot taken with the 550D will appear to have more magnification, resulting from the higher pixel density.

1) it no longer seems to get as close because you lose your 1.6 (note a kenko 1.4 TC will nearly fix this nicely you can also stack it with the extension tubes to get closer still) kenko TC will work with any EF lens unlike the canon ones.2) the Dof will seem unbelievably shallow so you are going to want to stop down anyway therefore adding a TC into the mix wont hurt

I had the 100mm non-L and now upgraded to the L, but I'd advise anyone to get the Kenko 1.4x in any case, even on crop it's a great addition. The only problem with the non-L and the tc is that the af fails when the aperture drop is too large at very close macro distances, this didn't happen to me with the L.

Adding 1.4x TC adds a bunch of extra lens elements to the optic pathway, so I prefer to add (hollow) extension tubes to my 100L Macro lens if I want more magnfication. The Pro-Optic extension tubes from Adorama are built well and cheap!

Adding 1.4x TC adds a bunch of extra lens elements to the optic pathway, so I prefer to add (hollow) extension tubes to my 100L Macro lens if I want more magnfication. The Pro-Optic extension tubes from Adorama are built well and cheap!

If you say "prefer" you have a tc on the macro, too? I just met a pro photog who only uses 1.4x and 2x tcs on his Nikon macro and wouldn't want it any other way.

I like the small tc because given the excellent iq of the 100L, the iq hit is near to unnoticeable, it works like a real 140mm lens at all focus distances (I'm dual-using the 100L for other shots, too) and the working distance for macro increases which is convenient for bugs and the like.

I'm thinking about getting a 2x tc for this macro lens, too - you could say I should get the 180mm macro, but the 100L is cheaper, has IS and the tc solution seems much more flexible to me, and vanilla external flashes work better with the tc solution.

Adding 1.4x TC adds a bunch of extra lens elements to the optic pathway, so I prefer to add (hollow) extension tubes to my 100L Macro lens if I want more magnfication. The Pro-Optic extension tubes from Adorama are built well and cheap!

if you stop it down a few stops the IQ hit is barely noticable so for macro almost a non issueeven at f8 or f11 the DoF is very very thin in macro

But between the aperture lost from the extension tube, and the aperture lost from closing down the lens, you're sacrificing a good bit of light which would have been helpful to take the picture. Macro is one of those times you can never have enough light. Plus, it's nice to shoot wide-open or nearly so when going macro - depending on the lens some have nicer OOF highlights wide open.